data_8G2I # _model_server_result.job_id hw1Q5MZdL-X3C1IrjUg_ug _model_server_result.datetime_utc '2025-02-27 07:54:41' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8g2i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8G2I # _exptl.entry_id 8G2I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 696.598 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8G2I _cell.length_a 86.659 _cell.length_b 86.659 _cell.length_c 137.066 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G2I _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_554 -x,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -45.688667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C30 H38 Br N11 O4' _chem_comp.formula_weight 696.598 _chem_comp.id I0B _chem_comp.mon_nstd_flag . _chem_comp.name "5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C11 C12 I0B sing 152 n n C11 N7 I0B sing 153 n n C13 C12 I0B doub 154 n y C13 C14 I0B sing 155 n y C12 C17 I0B sing 156 n y N7 C10 I0B sing 157 n n C14 C15 I0B doub 158 n y C10 O1 I0B doub 159 n n C10 N6 I0B sing 160 n n O2 C28 I0B sing 161 n n C17 C16 I0B doub 162 n y C15 C16 I0B sing 163 n y N6 C9 I0B sing 164 n n O3 C29 I0B sing 165 n n N2 C1 I0B doub 166 n y N2 C2 I0B sing 167 n y C9 C8 I0B sing 168 n n C1 N1 I0B sing 169 n y C28 C29 I0B sing 170 n n C28 C6 I0B sing 171 n n C5 C29 I0B sing 172 n n C5 O I0B sing 173 n n C5 N4 I0B sing 174 n n C6 O I0B sing 175 n n C6 C7 I0B sing 176 n n C2 N4 I0B sing 177 n y C2 C3 I0B doub 178 n y N1 C I0B doub 179 n y N4 C4 I0B sing 180 n y C8 N5 I0B sing 181 n n N5 C7 I0B sing 182 n n N5 C18 I0B sing 183 n n C C3 I0B sing 184 n y C N I0B sing 185 n n C3 N3 I0B sing 186 n y C4 N3 I0B doub 187 n y C18 C19 I0B sing 188 n n C19 C20 I0B sing 189 n n BR C24 I0B sing 190 n n C23 C24 I0B doub 191 n y C23 C22 I0B sing 192 n y N9 C21 I0B sing 193 n n N9 C22 I0B sing 194 n n N8 C21 I0B sing 195 n n N8 C20 I0B sing 196 n n C24 C25 I0B sing 197 n y C21 N10 I0B doub 198 n n C22 C27 I0B doub 199 n y C25 C26 I0B doub 200 n y C27 C26 I0B sing 201 n y C7 H1 I0B sing 202 n n C7 H2 I0B sing 203 n n C8 H3 I0B sing 204 n n C8 H4 I0B sing 205 n n C9 H5 I0B sing 206 n n C9 H6 I0B sing 207 n n C1 H7 I0B sing 208 n n C5 H8 I0B sing 209 n n C6 H9 I0B sing 210 n n C4 H10 I0B sing 211 n n O3 H11 I0B sing 212 n n C23 H12 I0B sing 213 n n C25 H13 I0B sing 214 n n C26 H14 I0B sing 215 n n C27 H15 I0B sing 216 n n N9 H16 I0B sing 217 n n N10 H17 I0B sing 218 n n N8 H18 I0B sing 219 n n C20 H19 I0B sing 220 n n C20 H20 I0B sing 221 n n C19 H21 I0B sing 222 n n C19 H22 I0B sing 223 n n C18 H23 I0B sing 224 n n C18 H24 I0B sing 225 n n C28 H26 I0B sing 226 n n O2 H27 I0B sing 227 n n C29 H28 I0B sing 228 n n N H29 I0B sing 229 n n N H30 I0B sing 230 n n N6 H31 I0B sing 231 n n N7 H32 I0B sing 232 n n C11 H33 I0B sing 233 n n C11 H34 I0B sing 234 n n C17 H35 I0B sing 235 n n C16 H36 I0B sing 236 n n C15 H37 I0B sing 237 n n C14 H38 I0B sing 238 n n C13 H39 I0B sing 239 n n # _atom_sites.entry_id 8G2I _atom_sites.fract_transf_matrix[1][1] 0.011539 _atom_sites.fract_transf_matrix[1][2] 0.006662 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013325 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007296 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 I0B A 1 501 501 I0B XXX . C 3 UNX A 1 502 1001 UNX UNX . D 3 UNX A 1 503 1002 UNX UNX . E 4 HOH A 1 601 32 HOH HOH . E 4 HOH A 2 602 23 HOH HOH . E 4 HOH A 3 603 45 HOH HOH . E 4 HOH A 4 604 31 HOH HOH . E 4 HOH A 5 605 41 HOH HOH . E 4 HOH A 6 606 26 HOH HOH . E 4 HOH A 7 607 40 HOH HOH . E 4 HOH A 8 608 46 HOH HOH . E 4 HOH A 9 609 12 HOH HOH . E 4 HOH A 10 610 13 HOH HOH . E 4 HOH A 11 611 36 HOH HOH . E 4 HOH A 12 612 4 HOH HOH . E 4 HOH A 13 613 14 HOH HOH . E 4 HOH A 14 614 22 HOH HOH . E 4 HOH A 15 615 20 HOH HOH . E 4 HOH A 16 616 10 HOH HOH . E 4 HOH A 17 617 18 HOH HOH . E 4 HOH A 18 618 16 HOH HOH . E 4 HOH A 19 619 17 HOH HOH . E 4 HOH A 20 620 27 HOH HOH . E 4 HOH A 21 621 3 HOH HOH . E 4 HOH A 22 622 48 HOH HOH . E 4 HOH A 23 623 19 HOH HOH . E 4 HOH A 24 624 33 HOH HOH . E 4 HOH A 25 625 37 HOH HOH . E 4 HOH A 26 626 24 HOH HOH . E 4 HOH A 27 627 30 HOH HOH . E 4 HOH A 28 628 43 HOH HOH . E 4 HOH A 29 629 1 HOH HOH . E 4 HOH A 30 630 44 HOH HOH . E 4 HOH A 31 631 15 HOH HOH . E 4 HOH A 32 632 50 HOH HOH . E 4 HOH A 33 633 38 HOH HOH . E 4 HOH A 34 634 11 HOH HOH . E 4 HOH A 35 635 49 HOH HOH . E 4 HOH A 36 636 29 HOH HOH . E 4 HOH A 37 637 21 HOH HOH . E 4 HOH A 38 638 35 HOH HOH . E 4 HOH A 39 639 25 HOH HOH . E 4 HOH A 40 640 39 HOH HOH . E 4 HOH A 41 641 7 HOH HOH . E 4 HOH A 42 642 42 HOH HOH . E 4 HOH A 43 643 9 HOH HOH . E 4 HOH A 44 644 34 HOH HOH . E 4 HOH A 45 645 28 HOH HOH . E 4 HOH A 46 646 5 HOH HOH . E 4 HOH A 47 647 8 HOH HOH . E 4 HOH A 48 648 47 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 I0B . . . B 2 6.935 19.904 -29.544 1 42.25 ? N1 I0B 501 A 1 HETATM 2 C C7 I0B . . . B 2 2.348 26.001 -28.338 1 42.97 ? C7 I0B 501 A 1 HETATM 3 C C8 I0B . . . B 2 2.322 28.26 -29.136 1 41.98 ? C8 I0B 501 A 1 HETATM 4 N N2 I0B . . . B 2 5.412 21.392 -30.677 1 40.24 ? N2 I0B 501 A 1 HETATM 5 C C9 I0B . . . B 2 1.939 28.416 -30.559 1 40.59 ? C9 I0B 501 A 1 HETATM 6 O O1 I0B . . . B 2 1.267 30.722 -31.812 1 41.43 ? O1 I0B 501 A 1 HETATM 7 C C1 I0B . . . B 2 6.54 20.682 -30.558 1 50.92 ? C1 I0B 501 A 1 HETATM 8 C C5 I0B . . . B 2 2.852 23.006 -30.041 1 44.16 ? C5 I0B 501 A 1 HETATM 9 C C6 I0B . . . B 2 2.496 25.268 -29.656 1 42.34 ? C6 I0B 501 A 1 HETATM 10 N N3 I0B . . . B 2 3.877 20.571 -27.556 1 48.57 ? N3 I0B 501 A 1 HETATM 11 C C4 I0B . . . B 2 3.022 21.392 -28.121 1 47.63 ? C4 I0B 501 A 1 HETATM 12 C C3 I0B . . . B 2 4.92 20.501 -28.467 1 42.87 ? C3 I0B 501 A 1 HETATM 13 O O3 I0B . . . B 2 0.745 22.379 -30.985 1 46.44 ? O3 I0B 501 A 1 HETATM 14 C C2 I0B . . . B 2 4.648 21.279 -29.585 1 45.53 ? C2 I0B 501 A 1 HETATM 15 N N4 I0B . . . B 2 3.432 21.88 -29.335 1 42.23 ? N4 I0B 501 A 1 HETATM 16 BR BR I0B . . . B 2 -3.067 35.377 -26 1 117.97 ? BR I0B 501 A 1 HETATM 17 C C24 I0B . . . B 2 -2.644 33.897 -24.909 1 63.71 ? C24 I0B 501 A 1 HETATM 18 C C23 I0B . . . B 2 -1.605 33.118 -25.32 1 56.19 ? C23 I0B 501 A 1 HETATM 19 C C25 I0B . . . B 2 -3.485 33.53 -23.856 1 74.9 ? C25 I0B 501 A 1 HETATM 20 C C26 I0B . . . B 2 -3.306 32.284 -23.256 1 70.19 ? C26 I0B 501 A 1 HETATM 21 C C27 I0B . . . B 2 -2.304 31.443 -23.713 1 63.57 ? C27 I0B 501 A 1 HETATM 22 C C22 I0B . . . B 2 -1.444 31.881 -24.738 1 61.9 ? C22 I0B 501 A 1 HETATM 23 N N9 I0B . . . B 2 -0.262 31.352 -25.233 1 38.42 ? N9 I0B 501 A 1 HETATM 24 C C21 I0B . . . B 2 -0.107 30.138 -24.85 1 47.46 ? C21 I0B 501 A 1 HETATM 25 N N10 I0B . . . B 2 -1.227 29.569 -24.319 1 44.3 ? N10 I0B 501 A 1 HETATM 26 N N8 I0B . . . B 2 1.014 29.601 -25.143 1 45.22 ? N8 I0B 501 A 1 HETATM 27 C C20 I0B . . . B 2 1.434 28.262 -24.805 1 40.84 ? C20 I0B 501 A 1 HETATM 28 C C19 I0B . . . B 2 1.941 27.659 -26.042 1 40.98 ? C19 I0B 501 A 1 HETATM 29 C C18 I0B . . . B 2 0.955 27.632 -27.212 1 41.59 ? C18 I0B 501 A 1 HETATM 30 N N5 I0B . . . B 2 1.548 27.2 -28.488 1 41.65 ? N5 I0B 501 A 1 HETATM 31 O O I0B . . . B 2 3.367 24.153 -29.422 1 41.93 ? O I0B 501 A 1 HETATM 32 C C28 I0B . . . B 2 1.205 24.683 -30.241 1 42.37 ? C28 I0B 501 A 1 HETATM 33 O O2 I0B . . . B 2 1.174 25.014 -31.617 1 40.76 ? O2 I0B 501 A 1 HETATM 34 C C29 I0B . . . B 2 1.33 23.182 -29.965 1 44.3 ? C29 I0B 501 A 1 HETATM 35 C C I0B . . . B 2 6.138 19.783 -28.467 1 49.24 ? C I0B 501 A 1 HETATM 36 N N I0B . . . B 2 6.56 19.005 -27.454 1 38.89 ? N I0B 501 A 1 HETATM 37 N N6 I0B . . . B 2 2.901 29.233 -31.297 1 38.71 ? N6 I0B 501 A 1 HETATM 38 C C10 I0B . . . B 2 2.458 30.346 -31.911 1 45.08 ? C10 I0B 501 A 1 HETATM 39 N N7 I0B . . . B 2 3.398 31.016 -32.603 1 41.44 ? N7 I0B 501 A 1 HETATM 40 C C11 I0B . . . B 2 3.072 32.207 -33.39 1 44.02 ? C11 I0B 501 A 1 HETATM 41 C C12 I0B . . . B 2 3.143 33.512 -32.637 1 38.27 ? C12 I0B 501 A 1 HETATM 42 C C17 I0B . . . B 2 3.84 33.595 -31.438 1 35.31 ? C17 I0B 501 A 1 HETATM 43 C C16 I0B . . . B 2 3.959 34.799 -30.781 1 36.3 ? C16 I0B 501 A 1 HETATM 44 C C15 I0B . . . B 2 3.384 35.948 -31.309 1 38.48 ? C15 I0B 501 A 1 HETATM 45 C C14 I0B . . . B 2 2.709 35.876 -32.504 1 38.34 ? C14 I0B 501 A 1 HETATM 46 C C13 I0B . . . B 2 2.564 34.66 -33.152 1 37.45 ? C13 I0B 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #